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Mining cancer methylomes: prospects and challenges

Abstract

There are over 28 million CpG sites in the human genome. Assessing the methylation status of each of these sites will be required to understand fully the role of DNA methylation in health and disease. Genome-wide analysis, using arrays and high-throughput sequencing, has enabled assessment of large fractions of the methylome, but each protocol comes with unique advantages and disadvantages. Notably, except for whole-genome bisulfite sequencing, most commonly used genome-wide methods detect <5% of all CpG sites. Here, we discuss approaches for methylome studies and compare genome coverage of promoters, genes, and intergenic regions, and capacity to quantitate individual CpG methylation states. Finally, we examine the extent of published cancer methylomes that have been generated using genome-wide approaches.

Type Journal
ISBN 0168-9525 (Print) 0168-9525 (Linking)
Authors Stirzaker, C.; Taberlay, P. C.; Statham, A. L.; Clark, S. J.;
Garvan Authors Aaron Statham , Dr Clare Stirzaker , Dr Phillippa Taberlay , Prof Susan Clark
Publisher Name TRENDS GENET
Published Date 2014-01-01 00:00:00
Published Volume 30
Published Issue 2
Published Pages 75-84
URL http://www.ncbi.nlm.nih.gov/pubmed/24368016
Status Published In-print
OpenAccess Link https://publications.gimr.garvan.org.au/download.php?12442_12786/1-s2.0-S0168952513001959-main.pdf